The CLI seems to work only after a profile has Autostart enabled. If Autostart is off, the CLI does not return the existing profile on running:
/Applications/Pritunl.app/Contents/Resources/pritunl-client list
The client has system and user profiles. A system profile is stored under the root user outside the user home directories. A user profile is stored in the users home directory. Internally an autostart profile is a system profile. The CLI client will only manage system profiles.
This was done to migrate the GUI to the new CLI component because system profiles automatically start by default. After enabling autostart in the GUI the (system) label will be shown in the profile name.
With the newer version of the client the autostart for system profiles can be disabled with the pritunl-client disable <profile_id> command. If this is done the profile will still be shown with autostart enabled in the GUI client. This will be improved when the redesigned GUI client is finished.